Atherosclerosis is a complex disease leading to heart attack and stroke that has genetic and environmental causes. A major initiating factor is the oxidative modification of phospholipids (OxPLs) in the vessel wall. OxPLs accumulate in lesions, induce the activation of several pathways in vascular cells such as endothelial cells, and are biomarkers of coronary disease and death. Genome-wide association studies (GWAS) are identifying the genetic loci that confer risk. However, most are located in large non-protein coding regions. Whereas aberrant regulation is likely to confer risk, regulatory mechanisms remain poorly understood. This proposal aims 1) to identify the genomic regulatory elements that specify human endothelial cell (EC) identity and their responses to OxPLs and 2) to define how the functions of these regulatory elements are affected by natural genetic variation. In Aim 1, I will test the hypothesis that a handful of lineage-determining transcription factors (LDTFs) establish the majority of the EC-specific enhancers that confer transcriptional responses to OxPLs. This hypothesis is justified based on my recent findings in macrophages, which demonstrated that relatively simple combinations of macrophage (LDTFs) play dominant roles in establishing the regulatory landscape. Characteristics of LDTFs identified previously will be used to identify and validate EC LDTF candidates in these studies. Preliminary data suggests the members of the ETS, AP-1 and FOX transcription factor families mediate a large proportion of EC regulation. In Aim 1 I will also identify the transcription factors that mediate endothelial responses to OxPLs. These factors are hypothesized to bind in close vicinity to LDTFs. Aim 1 will be completed during the K99 phase of this award. In Aim 2, I will utilize a well-defined population of 50 genetically diverse primary EC cultures to build a data-driven regulatory network. Association mapping and transcription factor motif mutation analysis will identify the genetic variants that perturb regulatory function and pro-atherogenic expression programs. Then, I will relate non-coding regulatory variants that alter enhancer activity to human disease. I hypothesize that these variants are likely to be enriched at GWAS loci for coronary artery disease. In such cases, the functional regulatory variant and cell type mediating susceptibility will be identified. Aim 2 will be completed during the R00 phase. My long-term goal is to elucidate the genetic mechanisms that predispose individuals to develop complex diseases such as atherosclerosis as an independent investigator. In my career, I strive to achieve these goals by integrating the skills acquired during my training as a systems geneticist with my ongoing training in mechanistic gene regulation. I will continue to take advantage of the numerous opportunities in the UCSD research community to enhance my training. My publication record demonstrates the ability to integrate genetics with complex traits using innovative approaches in the mouse and human populations. With support from the diverse group of highly skilled mentors in this application I am optimistic that I will be successful on my pathway to independence.